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- PDB-8bhf: Cryo-EM structure of stalled rabbit 80S ribosomes in complex with... -

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Basic information

Entry
Database: PDB / ID: 8bhf
TitleCryo-EM structure of stalled rabbit 80S ribosomes in complex with human CCR4-NOT and CNOT4
Components
  • (40S ribosomal protein ...) x 18
  • (60S ribosomal protein ...) x 32
  • (Ribosomal protein ...) x 21
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 40S_SA_C domain-containing protein
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • CCR4-NOT transcription complex subunit 3
  • P-site tRNA
  • Plectin/S10 N-terminal domain-containing protein
  • TRASH domain-containing protein
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-60S ribosomal protein L40
  • Ubiquitin-like domain-containing protein
  • mRNA
  • nascent chain
KeywordsRIBOSOME / translational control / mRNA decay / deadenylation / ribosome stalling / human CCR4-NOT
Function / homology
Function and homology information


CCR4-NOT core complex / regulatory ncRNA-mediated gene silencing / ribosomal subunit / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / phagocytic cup / protein-RNA complex assembly / ribosomal small subunit export from nucleus / rough endoplasmic reticulum / translation regulator activity ...CCR4-NOT core complex / regulatory ncRNA-mediated gene silencing / ribosomal subunit / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / phagocytic cup / protein-RNA complex assembly / ribosomal small subunit export from nucleus / rough endoplasmic reticulum / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / cellular response to interleukin-4 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / P-body / spindle / cytoplasmic ribonucleoprotein granule / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / rhythmic process / positive regulation of canonical Wnt signaling pathway / large ribosomal subunit / regulation of translation / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / killing of cells of another organism / cytoplasmic translation / cell differentiation / tRNA binding / mitochondrial inner membrane / postsynaptic density / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / mRNA binding / apoptotic process / synapse / dendrite / regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / DNA binding / RNA binding / zinc ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
CCR4-Not complex component, Not N-terminal domain / CCR4-NOT complex, subunit 3/ 5 / Not1 N-terminal domain, CCR4-Not complex component / CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily / Not2/Not3/Not5 / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus ...CCR4-Not complex component, Not N-terminal domain / CCR4-NOT complex, subunit 3/ 5 / Not1 N-terminal domain, CCR4-Not complex component / CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily / Not2/Not3/Not5 / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L13e / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / Ribosomal protein L30e signature 1. / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L13e / Ribosomal protein L30/YlxQ / Ribosomal protein L41 / Ribosomal protein L41 / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19, eukaryotic / Ribosomal protein L19e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / : / Ribosomal protein L6e signature. / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L44e / Ribosomal protein S3Ae, conserved site / Ribosomal protein L44 / Ribosomal protein S3Ae signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S27a / Ribosomal protein L34e, conserved site / Ribosomal protein S27a / Ribosomal protein L34e signature. / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S27e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S3, eukaryotic/archaeal / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L36e signature. / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein S19e / Ribosomal protein S8e, conserved site / Ribosomal protein S19e / Ribosomal protein S8e signature. / Ribosomal_S19e / Ribosomal protein S6, eukaryotic
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / CCR4-NOT transcription complex subunit 3 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein uS11 / 40S ribosomal protein S24 / 60S ribosomal protein L36 / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / 40S ribosomal protein SA / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsAbsmeier, E. / Chandrasekaran, V. / O'Reilly, F.J. / Stowell, J.A.W. / Rappsilber, J. / Passmore, L.A.
Funding support United Kingdom, Germany, 5items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105192715 United Kingdom
German Research Foundation (DFG)429892960 Germany
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
Wellcome Trust203149 United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Cryo-EM structure of stalled rabbit 80S ribosomes in complex with human CCR4-NOT and CNOT4
Authors: Gangwar, S.P. / Yen, L.Y. / Yelshanskaya, M.V. / Korman, A. / Jones, D.R. / Sobolevsky, A.I.
History
DepositionOct 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.4Jul 2, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: Ribosomal protein L15
B1: 60S ribosomal protein L13a
C1: 60S ribosomal protein L17
D1: Ribosomal protein L18
E1: Ribosomal protein L19
F1: 60S ribosomal protein L18a
G1: 60S ribosomal protein L21
H1: 60S ribosomal protein L22
I1: 60S ribosomal protein L23
J1: TRASH domain-containing protein
K1: Ribosomal protein L23/L25 N-terminal domain-containing protein
L1: Ribosomal protein L26
M1: 60S ribosomal protein L27
N1: 60S ribosomal protein L27a
O1: 60S ribosomal protein L29
P1: 60S ribosomal protein L30
Q1: 60S ribosomal protein L31
R1: Ribosomal protein L32
S1: 60S ribosomal protein L35a
T1: 60S ribosomal protein L34
U1: 60S ribosomal protein L35
V1: 60S ribosomal protein L36
W1: Ribosomal protein L37
X1: 60S ribosomal protein L38
Y1: 60S ribosomal protein L39-like
Z1: Ubiquitin-60S ribosomal protein L40
a1: 60S ribosomal protein L41
b1: Ribosomal protein L36a like
c1: 60S ribosomal protein L37a
d1: 60S ribosomal protein L28
e1: 60S acidic ribosomal protein P0
f1: 60S ribosomal protein L12
l1: 60S ribosomal protein L10a
m1: mRNA
n1: CCR4-NOT transcription complex subunit 3
21: P-site tRNA
11: nascent chain
A2: 28S ribosomal RNA
B2: 5S ribosomal RNA
C2: 5.8S ribosomal RNA
A3: 18S ribosomal RNA
B3: 40S_SA_C domain-containing protein
C3: 40S ribosomal protein S3a
D3: 40S ribosomal protein S2
E3: Ribosomal protein S3
F3: 40S ribosomal protein S4
G3: Ribosomal protein S5
H3: 40S ribosomal protein S6
I3: 40S ribosomal protein S7
J3: 40S ribosomal protein S8
K3: Ribosomal protein S9 (Predicted)
L3: Plectin/S10 N-terminal domain-containing protein
M3: 40S ribosomal protein S11
N3: 40S ribosomal protein S12
O3: ribosomal protein uS15
P3: Ribosomal protein S14
Q3: 40S ribosomal protein S15
R3: Ribosomal protein S16
S3: 40S ribosomal protein S17
T3: 40S ribosomal protein S18
U3: 40S ribosomal protein S19
V3: Ribosomal protein S20
W3: 40S ribosomal protein S21
X3: Ribosomal protein S15a
Y3: Ribosomal protein S23
Z3: 40S ribosomal protein S24
a3: 40S ribosomal protein S25
b3: 40S ribosomal protein S26
c3: 40S ribosomal protein S27
d3: Ribosomal protein S28
e3: 40S ribosomal protein S29
f3: Ubiquitin-like domain-containing protein
g3: Ubiquitin-40S ribosomal protein S27a
h3: Ribosomal protein RACK1
j3: 60S ribosomal protein L8
k3: Ribosomal protein L3
l3: 60S ribosomal protein L4
m3: 60S ribosomal protein L5
n3: 60S ribosomal protein L6
o3: 60S ribosomal protein L7
p3: 60S ribosomal protein L7a
q3: 60S ribosomal protein L9
r3: Ribosomal protein L10
s3: 60S ribosomal protein L11
t3: 60S ribosomal protein L13
u3: 60S ribosomal protein L14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,706,651368
Polymers3,699,50986
Non-polymers7,142282
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Ribosomal protein ... , 21 types, 21 molecules A1D1E1K1L1R1W1b1E3G3K3O3P3R3V3X3Y3d3h3k3r3

#1: Protein Ribosomal protein L15


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#4: Protein Ribosomal protein L18


Mass: 21568.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: Protein Ribosomal protein L19


Mass: 21613.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TYL6
#11: Protein Ribosomal protein L23/L25 N-terminal domain-containing protein


Mass: 13727.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#12: Protein Ribosomal protein L26


Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#18: Protein Ribosomal protein L32


Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#23: Protein Ribosomal protein L37


Mass: 10090.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#28: Protein Ribosomal protein L36a like


Mass: 12198.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T040
#45: Protein Ribosomal protein S3


Mass: 25215.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#47: Protein Ribosomal protein S5


Mass: 21525.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#51: Protein Ribosomal protein S9 (Predicted)


Mass: 21649.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#55: Protein ribosomal protein uS15


Mass: 17057.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#56: Protein Ribosomal protein S14


Mass: 14544.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T1F0
#58: Protein Ribosomal protein S16


Mass: 16032.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#62: Protein Ribosomal protein S20


Mass: 11395.489 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#64: Protein Ribosomal protein S15a


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#65: Protein Ribosomal protein S23


Mass: 15626.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#70: Protein Ribosomal protein S28


Mass: 7007.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#74: Protein Ribosomal protein RACK1


Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#76: Protein Ribosomal protein L3


Mass: 45119.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#83: Protein Ribosomal protein L10 / Ribosomal protein L10 (Predicted)


Mass: 24511.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2

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60S ribosomal protein ... , 32 types, 32 molecules B1C1F1G1H1I1M1N1O1P1Q1S1T1U1V1X1Y1a1c1d1f1l1j3l3m3n3o3p3q3s3t3u3

#2: Protein 60S ribosomal protein L13a


Mass: 23144.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#3: Protein 60S ribosomal protein L17


Mass: 17758.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SCJ6
#6: Protein 60S ribosomal protein L18a


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#7: Protein 60S ribosomal protein L21


Mass: 18478.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#8: Protein 60S ribosomal protein L22


Mass: 11495.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#9: Protein 60S ribosomal protein L23


Mass: 14761.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#13: Protein 60S ribosomal protein L27


Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#14: Protein 60S ribosomal protein L27a


Mass: 16489.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#15: Protein 60S ribosomal protein L29


Mass: 13401.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#16: Protein 60S ribosomal protein L30


Mass: 10914.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#17: Protein 60S ribosomal protein L31


Mass: 12635.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#19: Protein 60S ribosomal protein L35a


Mass: 12449.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#20: Protein 60S ribosomal protein L34


Mass: 12994.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXG5
#21: Protein 60S ribosomal protein L35


Mass: 14435.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#22: Protein 60S ribosomal protein L36


Mass: 11888.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TBH2
#24: Protein 60S ribosomal protein L38


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U001
#25: Protein/peptide 60S ribosomal protein L39-like


Mass: 6324.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#27: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4
#29: Protein 60S ribosomal protein L37a


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#30: Protein 60S ribosomal protein L28


Mass: 14220.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#32: Protein 60S ribosomal protein L12


Mass: 16561.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7
#33: Protein 60S ribosomal protein L10a


Mass: 23599.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein 60S ribosomal protein L8


Mass: 26998.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#77: Protein 60S ribosomal protein L4


Mass: 41101.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#78: Protein 60S ribosomal protein L5


Mass: 34077.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#79: Protein 60S ribosomal protein L6


Mass: 28818.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#80: Protein 60S ribosomal protein L7


Mass: 26658.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SV32
#81: Protein 60S ribosomal protein L7a


Mass: 27351.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#82: Protein 60S ribosomal protein L9


Mass: 21627.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#84: Protein 60S ribosomal protein L11


Mass: 19399.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#85: Protein 60S ribosomal protein L13


Mass: 24200.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TKB3
#86: Protein 60S ribosomal protein L14


Mass: 16217.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12

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Protein , 8 types, 8 molecules J1Z1e1n1B3L3f3g3

#10: Protein TRASH domain-containing protein


Mass: 12267.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: Protein Ubiquitin-60S ribosomal protein L40


Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#31: Protein 60S acidic ribosomal protein P0


Mass: 21521.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SPK4
#35: Protein CCR4-NOT transcription complex subunit 3 / cDNA FLJ61662 / highly similar to CCR4-NOT transcription complex subunit 3


Mass: 28090.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT3
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: B7Z6J7
#42: Protein 40S_SA_C domain-containing protein


Mass: 24361.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJH8
#52: Protein Plectin/S10 N-terminal domain-containing protein


Mass: 11529.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#72: Protein Ubiquitin-like domain-containing protein


Mass: 6512.737 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9D9G5
#73: Protein Ubiquitin-40S ribosomal protein S27a


Mass: 7986.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22

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RNA chain , 6 types, 6 molecules m121A2B2C2A3

#34: RNA chain mRNA


Mass: 896.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#36: RNA chain P-site tRNA


Mass: 24456.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#38: RNA chain 28S ribosomal RNA


Mass: 1634382.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#39: RNA chain 5S ribosomal RNA


Mass: 38385.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_4
#40: RNA chain 5.8S ribosomal RNA


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_3
#41: RNA chain 18S ribosomal RNA


Mass: 547733.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Protein/peptide , 1 types, 1 molecules 11

#37: Protein/peptide nascent chain


Mass: 501.618 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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40S ribosomal protein ... , 18 types, 18 molecules C3D3F3H3I3J3M3N3Q3S3T3U3W3Z3a3b3c3e3

#43: Protein 40S ribosomal protein S3a


Mass: 24759.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#44: Protein 40S ribosomal protein S2


Mass: 24441.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#46: Protein 40S ribosomal protein S4


Mass: 29523.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#48: Protein 40S ribosomal protein S6


Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#49: Protein 40S ribosomal protein S7


Mass: 21629.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: Protein 40S ribosomal protein S8


Mass: 24003.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#53: Protein 40S ribosomal protein S11


Mass: 17586.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#54: Protein 40S ribosomal protein S12


Mass: 13048.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#57: Protein 40S ribosomal protein S15


Mass: 15115.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#59: Protein 40S ribosomal protein S17


Mass: 15250.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#60: Protein 40S ribosomal protein S18


Mass: 16898.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZI5
#61: Protein 40S ribosomal protein S19


Mass: 15611.003 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#63: Protein 40S ribosomal protein S21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#66: Protein 40S ribosomal protein S24


Mass: 14432.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T3D8
#67: Protein 40S ribosomal protein S25


Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#68: Protein 40S ribosomal protein S26


Mass: 11645.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#69: Protein 40S ribosomal protein S27


Mass: 9348.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#71: Protein 40S ribosomal protein S29


Mass: 6559.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4

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Non-polymers , 2 types, 282 molecules

#87: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 275 / Source method: obtained synthetically / Formula: Mg
#88: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ribosome complex / Type: RIBOSOME
Details: 80S rabbit ribosome in complex with human CNOT3 protein
Entity ID: #1-#86 / Source: MULTIPLE SOURCES
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 47.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19437 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01234715
ELECTRON MICROSCOPYf_angle_d1.056343958
ELECTRON MICROSCOPYf_dihedral_angle_d16.0681237
ELECTRON MICROSCOPYf_chiral_restr0.05542756
ELECTRON MICROSCOPYf_plane_restr0.0122567

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